% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (c) 1992-2001 Regents of the University of California, Santa Cruz % % Sequence Alignment and Modeling Software System % http://www.cse.ucsc.edu/research/compbio/sam.html % % ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- % R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: % Extension and analysis of the basic method, CABIOS 12:95-107, 1996. % K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dsspfoo.1.YCL047C.t2k-100-30-dssp-ebghstl Host: cc71 Fri Dec 6 11:36:24 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCL0/YCL047C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YCL047C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YCL047C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 259 nodes, 183.72 seconds % % Sequence scores selected if better than: % E-value (Emax 4.0e+01) (select_score=4) % % Simple: NLL-NULL using FIM probabilities % Reverse: NLL-NULL for the reverse sequence NULL model % Calculated when Simple < simple_threshold (0.00) % E-value on N (=7316) sequences: % N / (1 + exp(-(lambda(=1.6082) * Reverse)^tau(=0.7577))) % Calculated when Simple < simple_threshold (0.00) % Rescale E-values or use -dbsize for multiple scoring runs. % Scores sorted by E-value, best first % % Sequence ID Length Simple Reverse E-value X count 1kamA 194 -192.51 -163.87 1.62e-26 1k4mA 213 -172.92 -150.73 1.07e-24 1kkuA 279 -103.13 -73.61 4.93e-13 1b6tA 159 -70.88 -46.83 2.43e-08 1qjcA 158 -70.30 -46.01 3.45e-08 1f9aA 168 -70.45 -45.31 4.66e-08 1ej2A 181 -63.19 -37.81 1.27e-06 1g8fA 511 -58.41 -31.36 2.47e-05 1jhdA 396 -55.35 -25.70 3.78e-04 1cozA 129 -45.36 -23.19 1.33e-03 1hnjA 317 -36.35 -13.71 2.18e-01 1jihA 531 -36.87 -12.65 4.04e-01 1uaaA 673 -37.57 -12.61 4.14e-01 1eblA 317 -34.15 -12.24 5.13e-01 1hn9A 317 -33.95 -12.17 5.37e-01 1kewA 361 -34.87 -12.09 5.61e-01 1fnnA 389 -37.04 -11.69 7.14e-01 1esmA 316 -35.14 -11.67 7.21e-01 3csuA 310 -36.45 -11.65 7.30e-01 1efpB 252 -33.62 -11.48 8.09e-01 1eblB 317 -33.19 -11.44 8.32e-01 1ekxA 311 -35.92 -11.40 8.51e-01 1j9yA 385 -38.42 -11.15 9.88e-01 1adeA 431 -34.70 -11.04 1.06e+00 1at1A 310 -35.17 -10.92 1.14e+00 1qf5A 431 -34.19 -10.74 1.27e+00 1trb 320 -34.36 -10.54 1.43e+00 1jtkA 136 -31.27 -10.38 1.58e+00 1g0oA 283 -33.36 -10.25 1.71e+00 1k0mA 241 -31.70 -10.23 1.73e+00 1ybvA 283 -33.35 -10.17 1.80e+00 3aprE 325 -31.38 -10.15 1.82e+00 2apr 325 -31.38 -10.15 1.82e+00 1h61A 364 -33.31 -10.09 1.89e+00 1k0nA 241 -31.74 -9.94 2.07e+00 1e0tA 470 -35.26 -9.82 2.23e+00 1l2tA 235 -32.91 -9.78 2.29e+00 1jwyB 315 -35.60 -9.76 2.33e+00 1kqfA 1015 -34.34 -9.64 2.50e+00 1jx2B 315 -36.64 -9.59 2.58e+00 1id3B 102 -28.85 -9.57 2.62e+00 1f6bA 198 -34.34 -9.54 2.67e+00 1dpe 507 -33.21 -9.50 2.74e+00 1fl2A 310 -31.32 -9.47 2.78e+00 1g0cA 364 -33.01 -9.45 2.83e+00 1j6oA 268 -35.26 -9.43 2.86e+00 1bg6 359 -31.25 -9.40 2.91e+00 1eqjA 511 -35.09 -9.37 2.97e+00 1epxA 370 -32.88 -9.25 3.21e+00 1dkuA 317 -34.29 -9.22 3.26e+00 1ejjA 511 -34.90 -9.12 3.49e+00 1gajA 257 -31.12 -8.99 3.78e+00 1dkrA 317 -34.11 -8.97 3.83e+00 1g01A 364 -32.86 -8.95 3.86e+00 1ex7A 186 -30.17 -8.95 3.88e+00 1d2nA 272 -33.67 -8.94 3.89e+00 1dppA 507 -32.82 -8.93 3.92e+00 1nsf 273 -33.49 -8.92 3.96e+00 1jilA 420 -33.63 -8.91 3.97e+00 1ad1A 266 -31.70 -8.91 3.98e+00 2ercA 244 -30.00 -8.87 4.07e+00 1gz0A 253 -34.50 -8.84 4.15e+00 1g55A 343 -30.94 -8.71 4.51e+00 1ibsA 317 -33.67 -8.70 4.55e+00 1g57A 217 -31.64 -8.67 4.65e+00 1gdeA 389 -31.69 -8.62 4.78e+00 1bzyA 217 -37.11 -8.59 4.87e+00 1gd9A 389 -31.69 -8.58 4.91e+00 1ihoA 283 -31.56 -8.57 4.93e+00 1gky 187 -29.76 -8.53 5.08e+00 1qamA 244 -30.30 -8.50 5.16e+00 1hq3D 103 -27.85 -8.46 5.31e+00 1lv7A 257 -31.65 -8.36 5.65e+00 1jeqA 609 -35.53 -8.26 6.05e+00 1l8qA 324 -35.63 -8.25 6.09e+00 1g6hA 257 -30.02 -8.23 6.16e+00 1byb 495 -32.70 -8.22 6.20e+00 1ig8A 486 -32.48 -8.22 6.22e+00 1hyuA 521 -32.03 -8.21 6.24e+00 1jvnA 555 -32.31 -8.16 6.45e+00 1qhaA 917 -34.78 -8.16 6.46e+00 1kzhA 555 -33.58 -8.16 6.46e+00 2tpsA 227 -29.48 -8.15 6.48e+00 1kepA 348 -30.08 -8.15 6.50e+00 1hkcA 917 -35.43 -8.14 6.55e+00 1dgkN 917 -34.83 -8.12 6.63e+00 1i50C 318 -30.72 -8.07 6.83e+00 1aoiF 87 -26.57 -8.07 6.84e+00 16pk 415 -35.13 -8.04 6.96e+00 1czaN 917 -34.85 -8.04 6.98e+00 1li5A 461 -31.96 -8.02 7.05e+00 1e3mA 800 -32.41 -8.01 7.10e+00 1aoiB 87 -26.46 -8.00 7.16e+00 1hkbA 917 -35.15 -7.92 7.54e+00 1hzpA 335 -31.44 -7.87 7.78e+00 1qfjA 232 -33.21 -7.85 7.89e+00 1d4oA 184 -29.05 -7.82 8.04e+00 1ex2A 189 -28.80 -7.76 8.37e+00 2pfkA 320 -31.39 -7.71 8.66e+00 1pfkA 320 -31.49 -7.61 9.27e+00 1zrn 232 -30.16 -7.58 9.44e+00 2lbp 346 -31.04 -7.53 9.74e+00 2nsyA 271 -30.17 -7.52 9.80e+00 1fwcC 567 -31.37 -7.51 9.88e+00 1ih8A 271 -30.17 -7.51 9.90e+00 1jztA 246 -30.46 -7.50 9.99e+00 1f7sA 139 -27.42 -7.49 1.00e+01 1vid 221 -29.34 -7.48 1.01e+01 4ubpC 570 -31.26 -7.47 1.01e+01 6mhtA 327 -30.35 -7.46 1.02e+01 1nsyA 271 -30.09 -7.45 1.03e+01 1kqpA 271 -30.09 -7.45 1.03e+01 1dtwB 342 -30.93 -7.41 1.06e+01 8abp 306 -30.84 -7.39 1.07e+01 1scmB 145 -26.72 -7.34 1.11e+01 1uok 558 -33.41 -7.30 1.14e+01 1k77A 260 -31.65 -7.27 1.16e+01 1a5t 334 -29.94 -7.26 1.17e+01 1bcpB 199 -28.47 -7.25 1.17e+01 1ubpC 570 -31.10 -7.23 1.19e+01 1xyzA 347 -31.19 -7.22 1.20e+01 2liv 344 -30.97 -7.17 1.24e+01 1bi5A 389 -31.83 -7.16 1.25e+01 1keeC 1073 -32.71 -7.16 1.25e+01 1qpbA 563 -32.41 -7.16 1.25e+01 1thfD 253 -30.03 -7.15 1.26e+01 1mh9A 197 -28.76 -7.13 1.27e+01 1c3oC 1073 -32.48 -7.11 1.29e+01 1keeG 1073 -32.40 -7.08 1.32e+01 1a9xA 1058 -32.26 -7.08 1.32e+01 2cbf 234 -31.11 -7.05 1.35e+01 1kk1A 410 -38.63 -7.03 1.37e+01 1alvA 173 -28.34 -6.99 1.40e+01 1jdbB 1073 -32.41 -6.96 1.44e+01 1i88A 389 -31.82 -6.94 1.45e+01 1qfnA 85 -25.78 -6.93 1.46e+01 1es9A 232 -33.41 -6.89 1.50e+01 1sup 275 -28.29 -6.88 1.51e+01 1qqtA 551 -29.66 -6.87 1.53e+01 1jkiA 533 -30.80 -6.86 1.53e+01 1et0A 269 -28.02 -6.85 1.54e+01 1k8eA 345 -29.92 -6.83 1.56e+01 1o17A 345 -29.92 -6.83 1.56e+01 1kgdA 180 -29.66 -6.81 1.59e+01 1mldA 314 -29.73 -6.81 1.59e+01 1pjr 724 -36.53 -6.80 1.59e+01 1qh3A 260 -28.17 -6.80 1.60e+01 1b9zA 516 -30.56 -6.80 1.60e+01 1qfcA 306 -28.55 -6.79 1.61e+01 1knqA 175 -28.49 -6.78 1.62e+01 1qh5A 260 -28.15 -6.77 1.62e+01 1tia 279 -28.58 -6.77 1.63e+01 1dbqA 289 -33.80 -6.76 1.65e+01 1f4lA 551 -29.66 -6.74 1.66e+01 3uagA 437 -30.83 -6.73 1.68e+01 1wer 334 -29.52 -6.73 1.68e+01 1c9uA 454 -29.66 -6.68 1.73e+01 1c3oA 1073 -32.13 -6.67 1.75e+01 1tsm 316 -29.18 -6.66 1.76e+01 1qb7A 236 -30.01 -6.66 1.76e+01 1wdcB 156 -27.20 -6.63 1.79e+01 1keeA 1073 -32.19 -6.63 1.80e+01 1pydA 556 -32.30 -6.63 1.80e+01 1fjxA 327 -29.62 -6.61 1.82e+01 1bxrA 1073 -32.17 -6.61 1.82e+01 1egaA 301 -32.86 -6.59 1.84e+01 1c3oG 1073 -31.91 -6.58 1.85e+01 1thg 544 -32.89 -6.58 1.86e+01 1jr3E 334 -29.48 -6.58 1.86e+01 1ofgA 381 -31.09 -6.57 1.86e+01 1i86A 389 -31.13 -6.51 1.94e+01 1cs0C 1073 -32.40 -6.51 1.95e+01 1qklA 127 -26.12 -6.49 1.97e+01 1php 394 -29.78 -6.46 2.01e+01 1pvdA 537 -32.12 -6.44 2.04e+01 9gafA 295 -28.22 -6.44 2.05e+01 4uagA 437 -30.65 -6.39 2.12e+01 1uag 437 -30.65 -6.37 2.15e+01 1e3dB 542 -28.91 -6.36 2.15e+01 1gt91 357 -30.02 -6.36 2.16e+01 1grx 85 -24.42 -6.35 2.18e+01 1ezm 301 -27.59 -6.32 2.22e+01 1a0cA 438 -29.27 -6.30 2.25e+01 1reqD 637 -32.17 -6.29 2.26e+01 1rie 129 -25.91 -6.28 2.27e+01 1jkmA 358 -28.83 -6.28 2.28e+01 1h2vZ 156 -26.79 -6.27 2.29e+01 1wab 232 -32.84 -6.26 2.31e+01 1ijbA 202 -28.78 -6.25 2.32e+01 1bxkA 355 -29.30 -6.23 2.36e+01 1ekeA 230 -28.85 -6.22 2.38e+01 1jq5A 370 -27.86 -6.21 2.39e+01 1keeE 1073 -31.60 -6.21 2.40e+01 1h6dA 433 -31.10 -6.21 2.40e+01 1c3oE 1073 -31.67 -6.20 2.41e+01 2btvA 901 -30.69 -6.20 2.42e+01 1i6wA 181 -27.10 -6.19 2.43e+01 1scuA 288 -31.02 -6.17 2.46e+01 1qnxA 209 -28.11 -6.15 2.50e+01 1i9sA 210 -28.60 -6.15 2.51e+01 2ts1 419 -30.43 -6.10 2.58e+01 1iv3A 152 -26.79 -6.10 2.59e+01 1b78A 193 -28.98 -6.08 2.62e+01 4ts1A 319 -28.86 -6.05 2.68e+01 1qfrA 89 -24.93 -6.04 2.69e+01 1jeyA 609 -32.81 -6.02 2.73e+01 1h6kZ 98 -25.83 -6.01 2.76e+01 1k1gA 131 -26.32 -6.01 2.76e+01 1bjwA 382 -30.00 -5.98 2.80e+01 1auq 208 -28.89 -5.98 2.81e+01 1qf6A 642 -30.56 -5.97 2.83e+01 1j9jA 247 -28.68 -5.97 2.84e+01 1ek6A 348 -30.40 -5.95 2.87e+01 1l9xA 315 -27.67 -5.95 2.88e+01 1oakA 196 -27.69 -5.93 2.92e+01 1qk8A 146 -27.91 -5.92 2.93e+01 1gnxA 479 -32.65 -5.90 2.97e+01 1tfr 305 -29.16 -5.90 2.97e+01 1akeA 214 -27.72 -5.90 2.98e+01 1cfzA 162 -26.33 -5.89 3.00e+01 1kyqA 274 -29.75 -5.88 3.01e+01 1f2dA 341 -29.84 -5.87 3.03e+01 1i19A 561 -29.56 -5.87 3.04e+01 1nfp 228 -29.52 -5.86 3.05e+01 1j5rA 371 -35.49 -5.86 3.05e+01 1qlmA 316 -29.80 -5.86 3.07e+01 1pjcA 361 -27.98 -5.85 3.08e+01 1ass 159 -25.85 -5.85 3.08e+01 1bdg 451 -30.79 -5.85 3.09e+01 1mjhB 162 -26.81 -5.84 3.10e+01 1gveA 327 -31.31 -5.84 3.11e+01 1qr7A 350 -31.34 -5.80 3.19e+01 8rucI 123 -26.69 -5.80 3.19e+01 1j8mF 297 -34.42 -5.79 3.21e+01 1jflA 228 -29.74 -5.79 3.21e+01 1rboC 123 -26.69 -5.78 3.24e+01 1hm9A 468 -28.54 -5.77 3.27e+01 3rubS 123 -27.77 -5.77 3.27e+01 1go4E 100 -24.87 -5.76 3.27e+01 1g97A 459 -28.57 -5.75 3.30e+01 1gg1A 350 -31.37 -5.75 3.31e+01 1qf9A 194 -28.58 -5.75 3.31e+01 1jx6A 342 -29.78 -5.73 3.34e+01 1fzqA 181 -29.89 -5.73 3.35e+01 1jqaA 370 -27.37 -5.72 3.37e+01 1fnsA 196 -28.23 -5.72 3.37e+01 1qjwA 365 -29.98 -5.70 3.43e+01 1klpA 115 -26.88 -5.69 3.44e+01 1dljA 402 -28.94 -5.68 3.47e+01 1hizA 379 -28.41 -5.68 3.48e+01 1ptf 88 -24.34 -5.66 3.52e+01 5ukdA 194 -28.50 -5.65 3.56e+01 1qbiA 454 -28.31 -5.64 3.58e+01 1bj4A 470 -28.92 -5.62 3.63e+01 2cb5A 453 -28.56 -5.62 3.63e+01 1lw6E 281 -26.87 -5.62 3.63e+01 1bn7A 294 -30.75 -5.61 3.65e+01 1dl5A 317 -28.59 -5.60 3.68e+01 1fhvA 323 -27.65 -5.59 3.70e+01 1a3c 181 -29.85 -5.59 3.70e+01 1i50B 1224 -32.96 -5.58 3.72e+01 6pfkA 319 -30.94 -5.58 3.72e+01 1asx 159 -25.69 -5.57 3.75e+01 1qlwA 328 -32.32 -5.56 3.78e+01 1mjhA 162 -27.06 -5.55 3.81e+01 1l1lA 739 -29.46 -5.54 3.83e+01 1deoA 233 -26.78 -5.54 3.84e+01 1kfuS 184 -26.45 -5.54 3.85e+01 1k7cA 233 -26.79 -5.53 3.87e+01 1exnB 290 -27.27 -5.53 3.88e+01 1h4vB 421 -29.33 -5.51 3.92e+01 1bvyF 191 -28.40 -5.51 3.93e+01 7reqB 637 -31.57 -5.51 3.93e+01 1poxA 585 -29.37 -5.49 3.99e+01